RetrogeneDB ID: retro_nleu_2138

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397331.1:11625193..11625874(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: RPL7L1
• Ensembl ID: ENSNLEG00000004649
• Aliases: None
• Description: None

Sequence

>retro_nleu_2138
AAATGGCGGAGCAAGAGCAAAGCCCTGAAAGCCACCCAGGCAAAGCAGGCACTTTTGTCAAAGAAAGAGCAGAGGAAAGG
AAAAGGGCTCAGGTTTAAGCAACTGGAATCATTCCTACATGATTCCTGATGGCAGAAATGTGATAAAGTGCATCTCAGAC
GACTAGAAGTGAAACATCATGCCTTGGAATTGCCAGATAAACATTCCTTTGTTGTACGCATCGAAAGAATTGATGGCGTG
AGTTTACTGGTGCAGAGAACCATTGTGAGACTTTGCCTAAAGAAAATTTTTAGTGGTATCTTTGTAAAAGTCACCCCCCA
CAACCTAAAAATGCTGCTTATAGTGGAACCTTATGTGACCTGGGGATTTCCAAATCTGAAGTCTGTCGAAGAACTCATTT
TGAAACATGGACAAGCCAAGGTCAAGAATAAGACCATCCCTCTGACAGACAACACAGTGATTGAGAAGCACCTGGGGAAG
TTTGGTGTCATTTGCTTGGAAGACCTCATTCATGAAATTGCCTTCCCAGGGAAGCATTTCCAGGAGATCTCATGGTTCTT
GCGCCCTTTCCACCTCTCAGTGGCCTGTCATGCTACCAAAAATAGAGTGGGCTTCCTCAAGGAGATGGGCACACCTGGCT
ATCGGGGTGAAGGCATCAGTCAGCTCATCCGCCAGCTGAAC

Alignment

ORF - retro_nleu_2138 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.21 %
• Parental protein coverage: 89.8 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KKRKAYQALKATQAKQALLAKKEQKKGKGLRFKRLESFLHDSWRQIRDKVRLRRLEVKPHALELPDKHSL
          K.R....ALKATQAKQALL.KKEQ.KGKGLRFK.LESFLHDS..Q..DKV.LRRLEVK.HALELPDKHS.
Retrocopy KWRSKSKALKATQAKQALLSKKEQRKGKGLRFKQLESFLHDS*WQKCDKVHLRRLEVKHHALELPDKHS-

Parental  AFVVRIERIDGVSLLVQRTIARLRLKKIFSGVFVKVTPQNLKMLRIVEPYVTWGFPNLKSVRELILKRGQ
          .FVVRIERIDGVSLLVQRTI.RL.LKKIFSG.FVKVTP.NLKML.IVEPYVTWGFPNLKSV.ELILK.GQ
Retrocopy -FVVRIERIDGVSLLVQRTIVRLCLKKIFSGIFVKVTPHNLKMLLIVEPYVTWGFPNLKSVEELILKHGQ

Parental  AKVKNKTIPLTDNTVIEEHLGKFGVICLEDLIHEIAFPGKHFQEISWFLRPFHLSVARHATKNRVGFLKE
          AKVKNKTIPLTDNTVIE.HLGKFGVICLEDLIHEIAFPGKHFQEISWFLRPFHLSVA.HATKNRVGFLKE
Retrocopy AKVKNKTIPLTDNTVIEKHLGKFGVICLEDLIHEIAFPGKHFQEISWFLRPFHLSVACHATKNRVGFLKE

Parental  MGTPGYRGERINQLIRQLN
          MGTPGYRGE.I.QLIRQLN
Retrocopy MGTPGYRGEGISQLIRQLN

Legend:

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

Expression

RNA-Seq

Nomascus leucogenys was not studied using RNA-Seq expression data.

ChIP-Seq

Nomascus leucogenys was not studied using ChIP-Seq data.

EST

Nomascus leucogenys was not studied using EST data.

TSS

Nomascus leucogenys was not studied using FANTOM5 data.

Lab

retro_nleu_2138 was not experimentally validated.

Homology

Retrocopy orthology:

Nomascus leucogenys does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 26 parental genes, and 124 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,
Monodelphis domestica	ENSMODG00000019028	1 retrocopy	retro_mdom_1708,
Mustela putorius furo	ENSMPUG00000013296	1 retrocopy	retro_mputfur_1577,
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,
Nomascus leucogenys	ENSNLEG00000026615	8 retrocopies	retro_nleu_1012, retro_nleu_1459, retro_nleu_1696, retro_nleu_1853, retro_nleu_2479, retro_nleu_2603, retro_nleu_3, retro_nleu_901,
Otolemur garnettii	ENSOGAG00000012671	3 retrocopies	retro_ogar_1380, retro_ogar_3358, retro_ogar_3428,
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,
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,