RetrogeneDB ID: retro_cfam_1474

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 32:23934818..23936742(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000010697
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SUGP2
• Ensembl ID: ENSCAFG00000014431
• Aliases: SUGP2, SFRS14
• Description: SURP and G patch domain containing 2 [Source:HGNC Symbol;Acc:18641]

Sequence

>retro_cfam_1474
AGTGTCACACCCCTGCTCATGGCTTGCAATGCCTATGAGCTGAGTGTCAAGATGAAAACCCTCAGTAACCCCCTGGACTT
GGCTGTTGCCCTGGAGACCACCAATTCTCTCTGCCAGAAGTCTTTAGCCCTTTTGGGACAGACTTTCTCCTTGGCCTCTT
CTTTCCAGCAAGAGAAAATCTTAGAAGCTGTTGGCTTCCAAGATATAGCTCCCTCTCCTGCTGCATTTCCAAATTTTGAG
GACTCTACTCTGTTTGGGAGAGAATACATCGATCACCTGAAGGCCTGGCTGGTCACCAGTGGGTGTCCACTTCAGGTCAA
GAAAGCTGAACCTGAGCCTACCCAAGATGAGGAGAAAGTTGTTCCTCCTACCAAACCCAAAATTCAGGCCAAGTCTCCGA
GTGGTCTCAATGATGCTGTCCCCCAACGAGCAGATCACAAGGTGGTGGACACCATCGATCAGCTGGTCCCACTCGCATTG
TCAGAGGCAGCCTATCTCCCAAAGAGAGAGCTCTTCTCAAGGAGGACCCTGCTTACTGGTTTTTGTCTGATGACAGTAGT
CTGGAGTATAAATACTACAAATTGAAGCTGGCAGAAATGCAGCGGATACGCCACACCTTGCCAGGAGCAGATCAAAAGCC
AATAGCAGCAGAATGTGGGGTCTGGGCCATGCTGTATGCTTGGACAATCCGGAGCCTCAAGAAGAGGCTCCTCCCAGACC
TCCAGCGGGAGCTGCTCCGCACTCAAGGGCTTCTGGGCTGGAAGGTGAGGAAAGCAACCACTGGGACCCAGACCCTCCTC
TCCTCAAGCACCAGACTGAAACACCATGGCCGGCAGGCTCCAGGTTCATTGCAGGGAAAGCTGTCCCAGCCAGATGGAAA
TGATACTGTCAAGGACTGCCCACCTGACCCAGTTGGACCCTCTCTTGGGGACCCCAGCCCAGAAGTCTTGGGCCTATCCC
CCAAGCCAGCAGGAGCGGAAGTCTCTGAAGCTCCTCAATCCTCCTCTCCCTGCCCATCTGCTGACGTTGACATGAAGACA
ATGGAGACTGCAGAGAAACTGGCCAGATTTGTTGCTCAGATGGGACAAGAAATTGAACAATTCAGCGTAGAAAACAGTAC
TGACAACCCTGACTTGTGGTTTCTCCATGACCAAAATAGTTCAGCCTTCAAATTCTATCGAAAGAAAGTATTTGAACTAT
GCCATCAATTTGTTTTACATCATCTCCACTGAACCTCCACACCAGTGAGAGCACTGATTCTCAAGAGAGCCCCCTTGATC
CCATGGAAGGGGAAGGAGAGTTTGAAGATGAGCCCCCTCAGCATGAGGCTGAGTTGGAAAGCCCAGAGGTGATGCCTGAG
GAGGATGATGAAGACGAGGAAGATGAGGATGAGGAGGGGACCGAAGAGGCCTCCACTCCTAGAGGGGCCTCCAGGCAACC
AGGAGGGGCTGCCAAGTCCGAGGGCTATAAGGGCAGCCCCCCCCCGCCCCATGGCCTCCCGAGCGAGGCAGCCGAAGATG
GCCCGGCGGGTGCACCTGCCCTATCACAGGCCACCTCAGGGGCCTGCTTCCCTCGGAAGAGGGTCAGTAGCAGGTCCTTG
AAGGTTGGCATGATTCCGGCTCCAGAGAGGCTGTGTCTCATCCAGGAACCCAAAGTTCATGAACCAGTTCGAATTGCCTA
CGACAGACCTCGGGGTTGTCCCATGTCCAAAAAGAAGAAACCCAAGGATTTTGATTTCGCCCAGCAGAAGCTGACCGACA
AGAACCTGGGGTTCCAGATGCTGCAGAAGATGGGCTGGAAGGAGGGCCACGGCCTGGGCTCCTGTGGGAAGGGCATCAGG
GAGCCCGTCAGCATGGGAACTGCATCGGAAGGGGAAGCGTTAGGTGCTGACGGGCAGGAGCACAAGGAAGATACGTGTTC
CGTC

Alignment

ORF - retro_cfam_1474 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.01 %
• Parental protein coverage: 58.63 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SVTPLLMACNAYELSVKMKTLSNPLDLAVALETTNSLCRKSLALLGQTFSLASSFRQEKILEAVGLQDIA
          SVTPLLMACNAYELSVKMKTLSNPLDLAVALETTNSLC.KSLALLGQTFSLASSF.QEKILEAVG.QDIA
Retrocopy SVTPLLMACNAYELSVKMKTLSNPLDLAVALETTNSLCQKSLALLGQTFSLASSFQQEKILEAVGFQDIA

Parental  PSPAAFPNFEDSTLFGREYIDHLKAWLVTSGCPLQVKKAEPEPTQDEEKVVPPTKLEVQAKSPSGLSDAV
          PSPAAFPNFEDSTLFGREYIDHLKAWLVTSGCPLQVKKAEPEPTQDEEKVVPPTK...QAKSPSGL.DAV
Retrocopy PSPAAFPNFEDSTLFGREYIDHLKAWLVTSGCPLQVKKAEPEPTQDEEKVVPPTKPKIQAKSPSGLNDAV

Parental  PQRADHKVVDTIDQLVTRIVGGSLSPKERAL-LKEDPAYWFLSDDSS-LEYKYYKLKLAEMQRVSHTLPG
          PQRADHKVVDTIDQLV............R.L.L...........D.S.LEYKYYKLKLAEMQR..HTLPG
Retrocopy PQRADHKVVDTIDQLVPLALSEAAYLPKREL<LLKEDPAYWFLSDDSSLEYKYYKLKLAEMQRIRHTLPG

Parental  ADQKPTAAECAVRAMLYARTIRSLKKRLLPGRRRGLLRTQGLRGWKVRKATTGTQTLLSSGTRLKHHGRQ
          ADQKP.AAEC.V.AMLYA.TIRSLKKRLLP...R.LLRTQGL.GWKVRKATTGTQTLLSS.TRLKHHGRQ
Retrocopy ADQKPIAAECGVWAMLYAWTIRSLKKRLLPDLQRELLRTQGLLGWKVRKATTGTQTLLSSSTRLKHHGRQ

Parental  APGSLQRKLSQPDGNDTVKDCPPDPVGPSLGDPSPEVSGLSPKPAGAEVSEAPQSSSPCPSADVDMKTME
          APGSLQ.KLSQPDGNDTVKDCPPDPVGPSLGDPSPEV.GLSPKPAGAEVSEAPQSSSPCPSADVDMKTME
Retrocopy APGSLQGKLSQPDGNDTVKDCPPDPVGPSLGDPSPEVLGLSPKPAGAEVSEAPQSSSPCPSADVDMKTME

Parental  TAEKLARFVAQVGPEIEQFSIENSTDNPDLWFLHDQNSSAFKFYRKKVFELC-PSICFSSSPLNLHTSES
          TAEKLARFVAQ.G.EIEQFS.ENSTDNPDLWFLHDQNSSAFKFYRKKVFELC.PSICF.SSPLNLHTSES
Retrocopy TAEKLARFVAQMGQEIEQFSVENSTDNPDLWFLHDQNSSAFKFYRKKVFELC<PSICFTSSPLNLHTSES

Parental  ADSQESPLDPMEGEGEFEDEPPQHEAELESPEVMPEEDDEDEEDEDEDEEGTEEASTPRGASRQPGGAAK
          .DSQESPLDPMEGEGEFEDEPPQHEAELESPEVMPEEDDEDE..EDEDEEGTEEASTPRGASRQPGGAAK
Retrocopy TDSQESPLDPMEGEGEFEDEPPQHEAELESPEVMPEEDDEDE--EDEDEEGTEEASTPRGASRQPGGAAK

Parental  SEGYEG-SPPPDGLPSEAAEDGPAGAPALSQATSGACFPRKRVSSKSLKVGMIPAPKRLCLIQEPKVHEP
          SEGY.G......GLPSEAAEDGPAGAPALSQATSGACFPRKRVSS.SLKVGMIPAP.RLCLIQEPKVHEP
Retrocopy SEGYKGXXXXXXGLPSEAAEDGPAGAPALSQATSGACFPRKRVSSRSLKVGMIPAPERLCLIQEPKVHEP

Parental  VRIAYDRPRGRPVSKKKKPKDFDFAQQKLTDKNLGFQMLQKMGWKEGHGLGSCGKGIREPVSVGTASEGE
          VRIAYDRPRG.P.SKKKKPKDFDFAQQKLTDKNLGFQMLQKMGWKEGHGLGSCGKGIREPVS.GTASEGE
Retrocopy VRIAYDRPRGCPMSKKKKPKDFDFAQQKLTDKNLGFQMLQKMGWKEGHGLGSCGKGIREPVSMGTASEGE

Parental  GLGADGQEHKEDTFDV
          .LGADGQEHKEDT..V
Retrocopy ALGADGQEHKEDTCSV

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
SRP012049_cerebellum	0.00 RPM	108.40 RPM
SRP017611_brain	0.08 RPM	90.98 RPM
SRP017611_kidney	0.00 RPM	29.91 RPM
SRP017611_liver	0.15 RPM	19.43 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1474 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1474 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1474 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000014431	1 retrocopy	retro_cfam_1474 ,