RetrogeneDB ID: retro_mmus_1684

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 18:7549010..7549589(+)
• Located in intron of: ENSMUSG00000057440

Retrocopy information

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

Parental gene information

• Parental gene symbol: Mad2l1
• Ensembl ID: ENSMUSG00000029910
• Aliases: Mad2l1, AA673185, MAD2
• Description: MAD2 mitotic arrest deficient-like 1 [Source:MGI Symbol;Acc:MGI:1860374]

Sequence

>retro_mmus_1684
CGTGGGAGCGCAGAAATCGTGGCCGAGTTTTTCTCATTTGGCATCAACAGCATTTTGTATCAGCGTGGCATTTATCCGTC
GGAAACCTTTACTAGCGTGCAGAAATATGGACTCCCCTCGCTTGCACCTACTGACCCCGAGCACATAAAGCACCTCAATA
ACGCGGTGGAACAGCTAAAGGGGTGGCTGTACAAGAGCTCAGCGAAGAAACTGGTGCTGGTCATCTCAAACAGTGAAAGT
GGTGACATCCTTGAAAGATGGCAGTTTGATAATGAGTGTGACCAAACTGCAAAAGAGGAAGGTGTTCATAGAGAAAAGTC
CCAGAAAGCCATACAGGATGAAATCTGTTCAGTGATTGGACAGATTACAGCTCCTGGGACATTTCTGCCACTGTTGGAAG
TTTCTTGTTCATTTGATCTGCTGATTTACACTGACAAAGACTTGGTGGTACCTGGAAAGTGGGAAGAATCGGGACCCCAG
TTTATTACCAGTTCTGAAGAAATCCGTCTACGCTGATTTACAACCACAAGCCACAAAGGGAATAAATAGTATGGTGGCCT
ACAAAACCCCATCAATGAA

Alignment

ORF - retro_mmus_1684 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.27 %
• Parental protein coverage: 93.66 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RGSAEIVAEFFSFGINSILYQRGIYPSETFTRVQKYGLTLLTTTDPELIKYLNNVVEQLKEWLYKCSVQK
          RGSAEIVAEFFSFGINSILYQRGIYPSETFT.VQKYGL..L..TDPE.IK.LNN.VEQLK.WLYK.S..K
Retrocopy RGSAEIVAEFFSFGINSILYQRGIYPSETFTSVQKYGLPSLAPTDPEHIKHLNNAVEQLKGWLYKSSAKK

Parental  LVVVISNIESGEVLERWQFDIECDKTAKEEGVRREKSQKAIQDEIRSVIRQITATVTFLPLLEVSCSFDL
          LV.VISN.ESG..LERWQFD.ECD.TAKEEGV.REKSQKAIQDEI.SVI.QITA..TFLPLLEVSCSFDL
Retrocopy LVLVISNSESGDILERWQFDNECDQTAKEEGVHREKSQKAIQDEICSVIGQITAPGTFLPLLEVSCSFDL

Parental  LIYTDKDLVVPEKWEESGPQFITNCEEVRLRSFTTTIHKVNS-MVAYKTPVND
          LIYTDKDLVVP.KWEESGPQFIT..EE.RLR.FTTT.HK.N........P.N.
Retrocopy LIYTDKDLVVPGKWEESGPQFITSSEEIRLR*FTTTSHKGNK*YGGLQNPINE

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	0.02 RPM	4.58 RPM
SRP007412_cerebellum	0.04 RPM	2.95 RPM
SRP007412_heart	0.00 RPM	2.74 RPM
SRP007412_kidney	0.00 RPM	3.08 RPM
SRP007412_liver	0.00 RPM	1.67 RPM
SRP007412_testis	0.00 RPM	6.91 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1684 was not detected

EST

No EST(s) were mapped for retro_mmus_1684 retrocopy.

TSS

No TSS is located nearby retro_mmus_1684 retrocopy 5' end.

Lab

retro_mmus_1684 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1684 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 38 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012813	2 retrocopies	retro_chof_1340, retro_chof_2524,
Dasypus novemcinctus	ENSDNOG00000013456	1 retrocopy	retro_dnov_1348,
Erinaceus europaeus	ENSEEUG00000009629	1 retrocopy	retro_eeur_446,
Echinops telfairi	ENSETEG00000015756	1 retrocopy	retro_etel_724,
Homo sapiens	ENSG00000164109	2 retrocopies	retro_hsap_1350, retro_hsap_1707,
Gorilla gorilla	ENSGGOG00000002516	1 retrocopy	retro_ggor_1281,
Loxodonta africana	ENSLAFG00000029619	1 retrocopy	retro_lafr_1138,
Myotis lucifugus	ENSMLUG00000011092	8 retrocopies	retro_mluc_1242, retro_mluc_165, retro_mluc_1802, retro_mluc_1904, retro_mluc_1986, retro_mluc_2434, retro_mluc_609, retro_mluc_696,
Macaca mulatta	ENSMMUG00000004875	2 retrocopies	retro_mmul_1292, retro_mmul_1701,
Monodelphis domestica	ENSMODG00000018944	1 retrocopy	retro_mdom_633,
Mus musculus	ENSMUSG00000029910	2 retrocopies	retro_mmus_1684 , retro_mmus_2573,
Nomascus leucogenys	ENSNLEG00000009092	1 retrocopy	retro_nleu_1832,
Oryctolagus cuniculus	ENSOCUG00000008243	4 retrocopies	retro_ocun_1424, retro_ocun_1469, retro_ocun_1486, retro_ocun_752,
Otolemur garnettii	ENSOGAG00000004054	1 retrocopy	retro_ogar_199,
Pongo abelii	ENSPPYG00000015029	2 retrocopies	retro_pabe_1121, retro_pabe_1403,
Pan troglodytes	ENSPTRG00000016401	2 retrocopies	retro_ptro_1156, retro_ptro_925,
Ictidomys tridecemlineatus	ENSSTOG00000025410	2 retrocopies	retro_itri_1592, retro_itri_327,
Tupaia belangeri	ENSTBEG00000011065	3 retrocopies	retro_tbel_4460, retro_tbel_4666, retro_tbel_664,
Tursiops truncatus	ENSTTRG00000011017	1 retrocopy	retro_ttru_1754,