RetrogeneDB ID: retro_mmus_2359

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 4:69853946..69854390(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000085627
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Rpl7l1
• Ensembl ID: ENSMUSG00000063888
• Aliases: Rpl7l1, 1500016H10Rik
• Description: ribosomal protein L7-like 1 [Source:MGI Symbol;Acc:MGI:1913479]

Sequence

>retro_mmus_2359
ATGGCGGAGGAAGGGGAAAGAAAGAAGATCCCTTTGGTTCGAGAAAATCTCCTGAAAAAGAGGAAGGCTTATCAAGCCCT
CAAAGCCACTCAGGCCAAGCAGGCACTTTTGGCAAAGAGAGAGAGAAAAGGGAAACAATTCAGGTTCAGACGACTAGAAT
CTTTCGTGCATGATTCCTGGCGGCAGCAACGTGACAAGGTGCGTGTCCAGCGGCTGGAGGTGAAGCCTCGTGCTTTGGAG
GGGCCTGATCAACATTCCTTGGCCTTGGTTATACGCATGGAAAGGATTGAAGGAGTGAGTTTATTGGTAAAGAGCACCAT
CATGAAACTTGGTCTGAAGAAATTGTTCAGTGGTGTCTTTGTCAAGGTCACCCCTCAGAGTGTAAGAATGCTGCTCACGG
TGGAGCCTTATGTGACCTGGGGATTTCCAAATCTGAAGTCTGTC

Alignment

ORF - retro_mmus_2359 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.95 %
• Parental protein coverage: 60.16 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAEEGERKKIPLVPENLLKKRKAYQALKATQAKQALLAKRERKGKQFRFRRLESFVHDSWRQQRDKVRVQ
          MAEEGERKKIPLV.ENLLKKRKAYQALKATQAKQALLAKRERKGKQFRFRRLESFVHDSWRQQRDKVRVQ
Retrocopy MAEEGERKKIPLVRENLLKKRKAYQALKATQAKQALLAKRERKGKQFRFRRLESFVHDSWRQQRDKVRVQ

Parental  RLEVKPRALEVPDKHPLAFVIRMERIEGVSLLVKSTIMKLGLKKLFSGVFVKVTPQSVRMLRTVEPYVTW
          RLEVKPRALE.PD.H.LA.VIRMERIEGVSLLVKSTIMKLGLKKLFSGVFVKVTPQSVRML.TVEPYVTW
Retrocopy RLEVKPRALEGPDQHSLALVIRMERIEGVSLLVKSTIMKLGLKKLFSGVFVKVTPQSVRMLLTVEPYVTW

Parental  GFPNLKSV
          GFPNLKSV
Retrocopy GFPNLKSV

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain	0.19 RPM	30.54 RPM
SRP007412_cerebellum	0.43 RPM	32.96 RPM
SRP007412_heart	0.00 RPM	35.05 RPM
SRP007412_kidney	0.92 RPM	54.09 RPM
SRP007412_liver	0.55 RPM	53.99 RPM
SRP007412_testis	0.41 RPM	21.41 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2359 was not detected

EST

No EST(s) were mapped for retro_mmus_2359 retrocopy.

TSS

TSS No.	TSS Name	TSS expression level (Expr) in TPM range:
		no expression	0 < Expr ≤ 1	1 < Expr ≤ 5	5 < Expr ≤ 10	Expr > 10
TSS #1	TSS_106339	185 libraries	378 libraries	494 libraries	12 libraries	3 libraries

The graphical summary, for retro_mmus_2359 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1072 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Lab

retro_mmus_2359 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2359 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 31 parental genes, and 190 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012791	2 retrocopies	retro_amel_1260, retro_amel_243,
Bos taurus	ENSBTAG00000018478	2 retrocopies	retro_btau_588, retro_btau_816,
Canis familiaris	ENSCAFG00000001728	4 retrocopies	retro_cfam_1180, retro_cfam_1464, retro_cfam_1638, retro_cfam_330,
Choloepus hoffmanni	ENSCHOG00000000306	4 retrocopies	retro_chof_1168, retro_chof_1404, retro_chof_388, retro_chof_478,
Cavia porcellus	ENSCPOG00000021189	2 retrocopies	retro_cpor_1134, retro_cpor_653,
Dasypus novemcinctus	ENSDNOG00000013485	1 retrocopy	retro_dnov_689,
Equus caballus	ENSECAG00000003113	1 retrocopy	retro_ecab_998,
Erinaceus europaeus	ENSEEUG00000010431	1 retrocopy	retro_eeur_90,
Echinops telfairi	ENSETEG00000002419	3 retrocopies	retro_etel_1151, retro_etel_1823, retro_etel_542,
Felis catus	ENSFCAG00000009707	1 retrocopy	retro_fcat_143,
Homo sapiens	ENSG00000146223	22 retrocopies	retro_hsap_1285, retro_hsap_1291, retro_hsap_1602, retro_hsap_1623, retro_hsap_1661, retro_hsap_1836, retro_hsap_2201, retro_hsap_2389, retro_hsap_2735, retro_hsap_2845, retro_hsap_3053, retro_hsap_3068, retro_hsap_3077, retro_hsap_3187, retro_hsap_3250, retro_hsap_3373, retro_hsap_3556, retro_hsap_3641, retro_hsap_3846, retro_hsap_3957, retro_hsap_4770, retro_hsap_4827,
Gorilla gorilla	ENSGGOG00000009958	15 retrocopies	retro_ggor_1009, retro_ggor_1013, retro_ggor_1253, retro_ggor_1261, retro_ggor_1904, retro_ggor_2099, retro_ggor_2108, retro_ggor_2113, retro_ggor_2162, retro_ggor_2282, retro_ggor_2457, retro_ggor_2524, retro_ggor_2591, retro_ggor_2659, retro_ggor_2973,
Macaca mulatta	ENSMMUG00000021313	1 retrocopy	retro_mmul_11,
Monodelphis domestica	ENSMODG00000019028	1 retrocopy	retro_mdom_1708,
Mustela putorius furo	ENSMPUG00000013296	1 retrocopy	retro_mputfur_1577,
Mus musculus	ENSMUSG00000043716	15 retrocopies	retro_mmus_1232, retro_mmus_1345, retro_mmus_1631, retro_mmus_2549, retro_mmus_2562, retro_mmus_2798, retro_mmus_3259, retro_mmus_3305, retro_mmus_3440, retro_mmus_3547, retro_mmus_3552, retro_mmus_3685, retro_mmus_561, retro_mmus_595, retro_mmus_708,
Mus musculus	ENSMUSG00000063888	4 retrocopies	retro_mmus_2359 , retro_mmus_3172, retro_mmus_3626, retro_mmus_777,
Nomascus leucogenys	ENSNLEG00000004649	21 retrocopies	retro_nleu_1375, retro_nleu_1597, retro_nleu_1646, retro_nleu_1661, retro_nleu_2007, retro_nleu_2011, retro_nleu_2017, retro_nleu_2138, retro_nleu_2201, retro_nleu_2282, retro_nleu_2562, retro_nleu_2599, retro_nleu_2694, retro_nleu_2863, retro_nleu_2938, retro_nleu_332, retro_nleu_502, retro_nleu_536, retro_nleu_597, retro_nleu_711, retro_nleu_727,
Oryctolagus cuniculus	ENSOCUG00000003844	6 retrocopies	retro_ocun_1393, retro_ocun_1604, retro_ocun_1818, retro_ocun_278, retro_ocun_509, retro_ocun_598,
Otolemur garnettii	ENSOGAG00000012671	3 retrocopies	retro_ogar_1380, retro_ogar_3358, retro_ogar_3428,
Pongo abelii	ENSPPYG00000016619	21 retrocopies	retro_pabe_1064, retro_pabe_1069, retro_pabe_1315, retro_pabe_1341, retro_pabe_1370, retro_pabe_1379, retro_pabe_1457, retro_pabe_2078, retro_pabe_2154, retro_pabe_2354, retro_pabe_2527, retro_pabe_2543, retro_pabe_2598, retro_pabe_2609, retro_pabe_2644, retro_pabe_2988, retro_pabe_3053, retro_pabe_3259, retro_pabe_3410, retro_pabe_3714, retro_pabe_3753,
Pan troglodytes	ENSPTRG00000018175	23 retrocopies	retro_ptro_1074, retro_ptro_1088, retro_ptro_1127, retro_ptro_1162, retro_ptro_1671, retro_ptro_1849, retro_ptro_1927, retro_ptro_1987, retro_ptro_2069, retro_ptro_2076, retro_ptro_2198, retro_ptro_2257, retro_ptro_2293, retro_ptro_2416, retro_ptro_2466, retro_ptro_2622, retro_ptro_2686, retro_ptro_2916, retro_ptro_2933, retro_ptro_3212, retro_ptro_355, retro_ptro_878, retro_ptro_882,
Pteropus vampyrus	ENSPVAG00000008696	3 retrocopies	retro_pvam_1179, retro_pvam_1482, retro_pvam_975,
Rattus norvegicus	ENSRNOG00000016269	1 retrocopy	retro_rnor_2795,
Sorex araneus	ENSSARG00000005286	2 retrocopies	retro_sara_100, retro_sara_211,
Sarcophilus harrisii	ENSSHAG00000011219	1 retrocopy	retro_shar_216,
Sus scrofa	ENSSSCG00000026472	3 retrocopies	retro_sscr_198, retro_sscr_756, retro_sscr_807,
Ictidomys tridecemlineatus	ENSSTOG00000009841	2 retrocopies	retro_itri_1233, retro_itri_417,
Tarsius syrichta	ENSTSYG00000004848	16 retrocopies	retro_tsyr_1312, retro_tsyr_1340, retro_tsyr_1380, retro_tsyr_1399, retro_tsyr_1729, retro_tsyr_1914, retro_tsyr_1933, retro_tsyr_2161, retro_tsyr_357, retro_tsyr_455, retro_tsyr_469, retro_tsyr_581, retro_tsyr_606, retro_tsyr_642, retro_tsyr_703, retro_tsyr_856,
Tursiops truncatus	ENSTTRG00000006971	6 retrocopies	retro_ttru_1194, retro_ttru_171, retro_ttru_361, retro_ttru_498, retro_ttru_528, retro_ttru_915,
Vicugna pacos	ENSVPAG00000008894	2 retrocopies	retro_vpac_386, retro_vpac_584,