RetrogeneDB ID: retro_sscr_255

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 10:78173440..78174199(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: YBX1
• Ensembl ID: ENSSSCG00000028485
• Aliases: None
• Description: Y box binding protein 1 [Source:HGNC Symbol;Acc:8014]

Sequence

>retro_sscr_255
TTCATCAAAAGGAATGACACCAAGGAAGATGTATTTGTACACCAGACTGCCATAAAGAAGAATAACTCCAGGAAGTACCT
GGGCAGTGTAGGATATTGAGAGTCTGTGGAGTTTGATGTTGTTGAAGGAGAAAAAGGTACAGAGGCAGCAAATGTACAGG
CCCTGCTAGAGTTCCAGAAAAAGGCAGTAAATATGAAACAAACTATAACCATTACAGAGGCTATCCATATTGCAGGGTTC
CTCCATGCAATTACCAGCAGAATTGCCAGAATTGTGACAGTTGGGGAAAGAAAGAGAGATCAGAGAGCGCTCCTGAAGGC
CAGGCCCAACAGCTCTGGCCCTACCAGTCCTATCGCAGTTGAAGTTTCCCATTTTATGACATGATGTGACTGGATGGGCA
TTGACCACAGTATTCTAACCCTCCTGTGCAGGGAAAAGTGATGGAGGGTGCTGACAAGCAGGGTGCAGGAGAACTAGGGA
GAGAGTGAGACAGAATATGTATAAGGGCTATAGACCATGATTCAGCATGGACCCTCCATGCCAAAGACAACCCAGAGAGG
ATAGCAATAAAGAAGATAAGGAAAATCAAGAAGAAGAGACCCAAGGTCAGCAGTCACCTCAACTTCAGTATGGCCACAAT
TTCAATTACCAGACAGACACCCTGAAAACCCTAAACCATAAGATGACAAAGAGACAAAAGCAGATGAACAACCAGGTGAA
TATTCCTCTACTCTCAAGGCTGAGCAGGATGGAGCTGAG

Alignment

ORF - retro_sscr_255 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.09 %
• Parental protein coverage: 77.47 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  YLKLNDTKEDVFVHQTAIKKNNPRKYLRSVGDGETVEFDVVEGEKGAEAANV-TGPGGVPVQGSKYAADR
          ..K.NDTKEDVFVHQTAIKKNN.RKYL.SVG..E.VEFDVVEGEKG.EAANV.TGP..VP..GSKY....
Retrocopy FIKRNDTKEDVFVHQTAIKKNNSRKYLGSVGY*ESVEFDVVEGEKGTEAANV<TGPARVPEKGSKYETNY

Parental  NHYRRYPRRRGPPRNYQQNYQNSESGEKNEGSESAPEGQAQQRRPYRRRR---FPPYYMRRPYGRRPQYS
          NHYR.YP..R.PP.NYQQN.QN..S..K.E.SESAPEGQAQQ..PY...R...FP.Y.M....G..PQYS
Retrocopy NHYRGYPYCRVPPCNYQQNCQNCDSWGKKERSESAPEGQAQQLWPYQSYRS*SFPFYDMM*LDGH*PQYS

Parental  NPPVQGEVMEGADNQGAGEQGRP-VRQNVYRGYRPRFRRGPPRQRQPREDGNEEDKENQGDETQGQQPPQ
          NPPVQG.VMEGAD.QGAGE.GR..VRQN.Y.GYRP.F...PP.QRQPRED.N.EDKENQ..ETQGQQ.PQ
Retrocopy NPPVQGKVMEGADKQGAGELGRE<VRQNMYKGYRP*FSMDPPCQRQPREDSNKEDKENQEEETQGQQSPQ

Parental  RRYRRNFNYRR-RRPENPKPQDGKETKAADPPAENSSAPEAEQGGAE
          ..Y..NFNY...R.PENPKP.D.KETKA...P.E.SS...AEQ.GAE
Retrocopy LQYGHNFNYQT<RHPENPKP*DDKETKADEQPGEYSSTLKAEQDGAE

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
SRP014902_placenta	0.00 RPM	380.94 RPM
SRP014902_testis	0.00 RPM	472.15 RPM
SRP018288_heart	0.00 RPM	1122.29 RPM
SRP018288_kidney	0.00 RPM	348.32 RPM
SRP018288_liver	0.00 RPM	320.30 RPM
SRP018288_lung	0.00 RPM	573.38 RPM
SRP018856_adipose	0.00 RPM	1214.00 RPM
SRP035408_brain	0.00 RPM	705.69 RPM
SRP035408_liver	0.00 RPM	895.64 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_255 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_255 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_255 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 53 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000016627	1 retrocopy	retro_dord_625,
Echinops telfairi	ENSETEG00000004125	3 retrocopies	retro_etel_1772, retro_etel_1980, retro_etel_2134,
Loxodonta africana	ENSLAFG00000007597	1 retrocopy	retro_lafr_804,
Macaca mulatta	ENSMMUG00000013136	5 retrocopies	retro_mmul_1139, retro_mmul_1423, retro_mmul_2017, retro_mmul_423, retro_mmul_861,
Oryctolagus cuniculus	ENSOCUG00000028047	2 retrocopies	retro_ocun_1519, retro_ocun_1953,
Otolemur garnettii	ENSOGAG00000006784	25 retrocopies	retro_ogar_1127, retro_ogar_1246, retro_ogar_1350, retro_ogar_1371, retro_ogar_1497, retro_ogar_2011, retro_ogar_2018, retro_ogar_2302, retro_ogar_2359, retro_ogar_2607, retro_ogar_2654, retro_ogar_3170, retro_ogar_3225, retro_ogar_324, retro_ogar_3303, retro_ogar_3316, retro_ogar_3317, retro_ogar_3366, retro_ogar_3416, retro_ogar_3474, retro_ogar_448, retro_ogar_572, retro_ogar_678, retro_ogar_690, retro_ogar_753,
Ochotona princeps	ENSOPRG00000008050	11 retrocopies	retro_opri_1097, retro_opri_1114, retro_opri_115, retro_opri_1196, retro_opri_340, retro_opri_367, retro_opri_626, retro_opri_781, retro_opri_896, retro_opri_910, retro_opri_984,
Sorex araneus	ENSSARG00000007896	1 retrocopy	retro_sara_559,
Sus scrofa	ENSSSCG00000028485	3 retrocopies	retro_sscr_1157, retro_sscr_255 , retro_sscr_256,
Ictidomys tridecemlineatus	ENSSTOG00000000116	1 retrocopy	retro_itri_1532,