RetrogeneDB ID: retro_cpor_124

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_10:26307751..26308936(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCPOG00000006216
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: B4GALT2
• Ensembl ID: ENSCPOG00000007511
• Aliases: None
• Description: None

Sequence

>retro_cpor_124
ATGAGGTTTCAGGAGCAGCTACTGAGTGGCAGTGCCACATTGCCCTGTGGCTCCCTGTACCGTGCCTGTTGCCTGCTTGT
GGCCCTCTCTGCACTGCACTTTGGTGTCACCCTTGTCTACTACCTGTCCAGCCTCAACCTGAGCCACCTGCCCCGGCTAA
TTGGAGTCCCCACAACAGTACTGGGCATCGTTGCCAGCAGGCATCCCCCTCGGCAACCCCAGTCTGGAGTGACCTGGGCA
CTGCCTCCTTTGAATATCTCTGCTCAGCCTCTCCTGGGTCAAGTCTCCAGTCCTGGTGTGAATTCTGACCACAGCCCCAC
AAACAACTTGACTTCTGTCCCAATGTTCCCCACAAAAGCACTATTGCTGCCCACTTGCCCCAAGGAGTCCCCACTACTTA
TTGGACCCATGGTGATCAAATTTAACATCCCTGTGGATCTGGAATTTTTGGCAACACAGAATCCAGAGATAAGGATGGGC
GGCCGTTATACCCCCAAGGAATGCATCTCTCCTCACAAGGTGGCCATCATCATTCCATTCCGTAACCGGCAGGAGCACCT
CAAATATTTGCTGTATTATTTGCACCCCCTTCTACAGCGCCAACAATTAGACTATGGTATCTATGTTATCAACCAGGCTG
GAGACTATATATTCAATCGTGCTAAACTTCTCAATATTGGCTTTCAAGAAGCCTTAAAGGACTATGACTACAACTGCTTT
GTGTTCAGTGATGTGGACCTCATCCCAATGGATGATCATAATGCTTACAGGTGTTTTTCACAGCCACGACATATTTCTGT
TGCAATGGACAAGTTTGGATTTAGCCTGCCTTATGTTCAGTATTTTGGAGGTGTCTCTGCTCTAAGTAAACGACAGTTTA
TTATCATAAATGGATTTCCTAATAATTACTGGGGCTGGGGAGGAGAAGATGATGATATTTTTAACAGATTATCTCTTAAG
GGCATGTCTGTATCTCGCCCAAATGCTGTGGTTGGGAGGTATCGCATGTTCCGCCACTCAAAAGACAAGGAAAATGAACC
CAATCCTCAGAGGTTTGCCCAAAATGCACACACTGAGGAGACAATGTACTCTGATGGTTTGAACTCACTCACCTATCAGC
TGTTGGACATAGAGAGACACCAATTATATACAAAAATCACAGTGGATATTGGGACACCAACCTAG

Alignment

ORF - retro_cpor_124 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.86 %
• Parental protein coverage: 80.76 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SRPNATAPSSGLPEVPSARPGPT-APILPPCPDSPPGLVGRLLIEFTSPMPLERVQRENPGVLLGGRYTP
          S.P......S......S....PT.A..LP.CP...P.L.G...I.F..P..LE.....NP....GGRYTP
Retrocopy SSPGVNSDHSPTNNLTSVPMFPTKALLLPTCPKESPLLIGPMVIKFNIPVDLEFLATQNPEIRMGGRYTP

Parental  PDCTPAQTVAVIIPFRHREHHLRYWLHYLHPILRRQRLRYGIYVINQHGEDTFNRAKLLNVGFLEALKED
          ..C.....VA.IIPFR.R..HL.Y.L.YLHP.L.RQ.L.YGIYVINQ.G...FNRAKLLN.GF.EALK.D
Retrocopy KECISPHKVAIIIPFRNRQEHLKYLLYYLHPLLQRQQLDYGIYVINQAGDYIFNRAKLLNIGFQEALK-D

Parental  AAYDCFIFSDVDLVPMDDRNLYRCGDQPRHFAIAMDKFGFRLPYAGYFGGVSGLSKAQFLRINGFPNEYW
          ..Y.CF.FSDVDL.PMDD.N.YRC..QPRH...AMDKFGF.LPY..YFGGVS.LSK.QF..INGFPN.YW
Retrocopy YDYNCFVFSDVDLIPMDDHNAYRCFSQPRHISVAMDKFGFSLPYVQYFGGVSALSKRQFIIINGFPNNYW

Parental  GWGGEDDDIFNRISLTGMKISRPDIRIGRYRMIKHDRDKHNEPNPQRFTKIQNTKLTMKRDGIGSVRYQV
          GWGGEDDDIFNR.SL.GM..SRP....GRYRM..H..DK.NEPNPQRF.....T..TM..DG..S..YQ.
Retrocopy GWGGEDDDIFNRLSLKGMSVSRPNAVVGRYRMFRHSKDKENEPNPQRFAQNAHTEETMYSDGLNSLTYQL

Parental  LEVSRQPLFTNITVDIGRP
          L...R..L.T.ITVDIG.P
Retrocopy LDIERHQLYTKITVDIGTP

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
SRP017611_brain	0.12 RPM	57.40 RPM
SRP017611_kidney	0.10 RPM	8.79 RPM
SRP017611_liver	0.00 RPM	3.13 RPM
SRP040447_lung	0.58 RPM	19.65 RPM
SRP040447_skeletal_muscle	0.04 RPM	19.78 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_124 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_124 was not experimentally validated.

Homology

Retrocopy orthology:

Cavia porcellus 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000007511	1 retrocopy	retro_cpor_124 ,