RetrogeneDB ID: retro_btau_1035

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 23:49302305..49303199(-)
• Located in intron of: ENSBTAG00000031432

Retrocopy information

• Ensembl ID: ENSBTAG00000018309
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SDCBP
• Ensembl ID: ENSBTAG00000019910
• Aliases: None
• Description: syntenin-1 [Source:RefSeq peptide;Acc:NP_001068951]

Sequence

>retro_btau_1035
ATGTCTCTGTACCCATCTCTTGAAGACCTGAAGGTAGACAATGTGATTCAGGCTCAGACTGCCTTTTCTGCAAACCCTGC
CAACCCAGCGATTTTATCTGAAGCCTCTGCTCCCATCTCTCAAGATGGAAATCTCTATCCTAAGCTATATCCGGAGCTCT
CTCAGTACATGGGCCTGAGTTTAAATGAAGAAGAAATACATGTAAATATGGCCTTGGTCCCTGGAGCACCAAGTCAGGGG
GTGGTGGCGCGGCCTTCCAGCATGGTGGCCACATGGTGGCCCCTATCACTGGTGGCGACATTGGGATCCACAGAGCAGAG
ATCAAGCAAGGGATCCGGGAAGTCATCTTGTGTAAGGATCAAGACGGGAAGATTGGGCTCAGGCTGAAATCCATAGACAA
CGGTATATTTGTTCAGCTTGTCCAGGCCAATTCTCCGTCCTCCCTGGTGGGCCTGCGGTTTGGGGACCAGGTGCTGCAGA
TAAACGGCAAGAACTGTGCTGGCTGGAGCTCGGACCGGGCGCACAAGGTGCTCAAACAGGCTTTCGGAGAGATCATCACC
ATGACCATTCGGGACAGGCCCTTTGAACGGACAATTACCATGCATAAGGACAGTACTGGACACATTGGCTTTGTTTTTAA
AAATGGAAAAATCACATCCATTGTGAAAGACAGTTCTGCAGCTAGAAACCGTCTTCTCACGGAACATAACATCAGTGAGG
TCAAGGGACAGAACGTCATTGGACTGAAGGACTCTCAAATCGCAGACATATTGTCCACAGCTGGAAATATAGTTACTATT
ACAATCATGCCTGCTTTTAATCTTTGAACACATTATTAAACGGATGGCGCCAAGCATTATGAAAAGCTTGATGGATCACA
CCATTCCTGAGGTT

Alignment

ORF - retro_btau_1035 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93. %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSLYPSLEDLKVDKVIQAQTAFSANPANPAILSEASAPVSQDGNLYPKLYPELSQYMGLSLNEEEIRANM
          MSLYPSLEDLKVD.VIQAQTAFSANPANPAILSEASAP.SQDGNLYPKLYPELSQYMGLSLNEEEI..NM
Retrocopy MSLYPSLEDLKVDNVIQAQTAFSANPANPAILSEASAPISQDGNLYPKLYPELSQYMGLSLNEEEIHVNM

Parental  ALVPGAPSQGQVVARPSSM-NHMVAPITGGDIGIRRAEIKQGIREVILCKDQDGKIGLRLKSIDNGIFVQ
          ALVPGAPSQG.V....S....HMVAPITGGDIGI.RAEIKQGIREVILCKDQDGKIGLRLKSIDNGIFVQ
Retrocopy ALVPGAPSQGVVARPSSMV<GHMVAPITGGDIGIHRAEIKQGIREVILCKDQDGKIGLRLKSIDNGIFVQ

Parental  LVQANSPSSLVGLRFGDQVLQINGENCAGWSSDRAHKVLKQAFGEKITMTIRDRPFERTITMHKDSTGHV
          LVQANSPSSLVGLRFGDQVLQING.NCAGWSSDRAHKVLKQAFGE.ITMTIRDRPFERTITMHKDSTGH.
Retrocopy LVQANSPSSLVGLRFGDQVLQINGKNCAGWSSDRAHKVLKQAFGEIITMTIRDRPFERTITMHKDSTGHI

Parental  GFVFKNGKITSIVKDSSAARNGLLTEHNICEVNGQNVIGLKDSQIADILSTAGNIVTITIMPAF-IFEHI
          GFVFKNGKITSIVKDSSAARN.LLTEHNI.EV.GQNVIGLKDSQIADILSTAGNIVTITIMPAF.IFEHI
Retrocopy GFVFKNGKITSIVKDSSAARNRLLTEHNISEVKGQNVIGLKDSQIADILSTAGNIVTITIMPAF>IFEHI

Parental  IKRMAPSIMKSLMDHTIPEV
          IKRMAPSIMKSLMDHTIPEV
Retrocopy IKRMAPSIMKSLMDHTIPEV

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
ERP005899_liver	0.07 RPM	60.34 RPM
ERP005899_muscle	0.42 RPM	187.24 RPM
SRP017611_brain	0.96 RPM	117.53 RPM
SRP017611_kidney	1.96 RPM	203.24 RPM
SRP017611_liver	0.45 RPM	41.45 RPM
SRP030211_testis	0.13 RPM	93.49 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1035 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1035 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1035 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 33 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006161	1 retrocopy	retro_amel_654,
Bos taurus	ENSBTAG00000019910	2 retrocopies	retro_btau_1035 , retro_btau_383,
Canis familiaris	ENSCAFG00000007112	1 retrocopy	retro_cfam_112,
Choloepus hoffmanni	ENSCHOG00000003565	5 retrocopies	retro_chof_1063, retro_chof_1151, retro_chof_1910, retro_chof_713, retro_chof_970,
Equus caballus	ENSECAG00000015053	1 retrocopy	retro_ecab_439,
Homo sapiens	ENSG00000137575	2 retrocopies	retro_hsap_3971, retro_hsap_4810,
Gorilla gorilla	ENSGGOG00000009019	2 retrocopies	retro_ggor_2666, retro_ggor_2995,
Loxodonta africana	ENSLAFG00000010757	1 retrocopy	retro_lafr_1044,
Microcebus murinus	ENSMICG00000003968	1 retrocopy	retro_mmur_170,
Myotis lucifugus	ENSMLUG00000004807	1 retrocopy	retro_mluc_12,
Macaca mulatta	ENSMMUG00000017296	1 retrocopy	retro_mmul_2564,
Mustela putorius furo	ENSMPUG00000010339	5 retrocopies	retro_mputfur_1055, retro_mputfur_1340, retro_mputfur_292, retro_mputfur_829, retro_mputfur_933,
Nomascus leucogenys	ENSNLEG00000001408	2 retrocopies	retro_nleu_2185, retro_nleu_2525,
Otolemur garnettii	ENSOGAG00000013462	1 retrocopy	retro_ogar_3259,
Procavia capensis	ENSPCAG00000016432	1 retrocopy	retro_pcap_186,
Pongo abelii	ENSPPYG00000018612	3 retrocopies	retro_pabe_3265, retro_pabe_3266, retro_pabe_3738,
Pan troglodytes	ENSPTRG00000020277	2 retrocopies	retro_ptro_2696, retro_ptro_3200,
Tupaia belangeri	ENSTBEG00000013965	1 retrocopy	retro_tbel_2142,