RetrogeneDB ID: retro_btau_581

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 15:48307546..48309223(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GALNT1
• Ensembl ID: ENSBTAG00000011206
• Aliases: None
• Description: Polypeptide N-acetylgalactosaminyltransferase 1 Polypeptide N-acetylgalactosaminyltransferase 1 soluble form [Source:UniProtKB/Swiss-Prot;Acc:Q07537]

Sequence

>retro_btau_581
ATGAGAAAATTTGCATACTGCAAGGTGGTCCTAGCCACCTCCTTGATTTGGGTACTCTTGGATATGTTCCTGCTGCTTTA
CTTCAGTGAATGCAACAAATGTGATGAAAAAAAAGAGAGAGGACTTCCTGCTGGGGATGTTCTAGAGCCAGTACAAAAGC
CTCATGAAGGTCCTGGAGAAATGGGGAAACCAGTCGTCATTCCTAAACAGGATCAAGAAAAGATGAAAGACATGTTTAAA
ATCAATCAGTTCAATTTAATGGCAAGTGAGATGATTGCACTCAACAGATCTCTACCAGATGTTAGGTTAGAAGGGTGTAA
AACAAAGGTGTATCCAAATAACCTTCCTACAACCAGTGTGGTGATTGTTTTCCACAATGAGGCTTGGAGCACACTTCTGC
GAACTGTCCATAGCATCATTAATCACTCACCAAGGCACATGCTAGAAGAAATTGTTCTAGTAGATGATGCCAGTGAAAGA
GACTTTTTAAAAAGACCTCTAGAGAGTTAAGTGAAAAAATTAAAAGTACCCGTTCACGTCATTCGAATGGAGCAGCGTTC
TGGATTGATCAGAGCTAGGTTAAAAGGTGCTGCTGTGTCTAAAGGCCAAGTGACCACCTTTTTAGATGCGCACTGTGAGT
GCACAGTGGGGTGGCTGGAGCCTCTCTTAGCCAGGATCAAACACGACAGGAAGACAGTGGTCTGTCCCATCATAGATGTG
ATCAGTGATGACACTTTCGAGTACATGGCAGGTTCTGACATGACCTATGGTGGGTTCAACTGGAAGCTCAACTTTCGCTG
GTATCCTGTTCCCCAAAGAGAAATGGACAGAAGGAAAGGTGATCGGACTCTTCCTGTGAGAACACCTACAATGGCAGGAG
GCCTTTTCTCAATAGACAGAGATTACTTTCAGGAAACTGGAACATATGATGCTGGAATGGATATTTGGGGAGGAGAAAAC
CTAGAAATTTCCTTTAGGATTTGGCAGTGTGGAGGAACTTTGGAGATTGTTACTTGCTCACATGTTGGACATGTGTTTCG
GAAAGCTACACCCTACACGTTTCCAGGAGGCACGGGGCAGATTATCAATAAAAATAACAGACGACTTGCAGAAGTATGGA
TGGATGAATTCAAGAATTTCTTCTATATAATTTCTCCAGGTGTTACAAAGGTAGATTATGGAGATATATCATCAAGACTT
GGTCTAAGGCACAAACTCCAATGCAGACCATTCTCTTGGTACCTAGAGAATATTTATCCTGATTCTCAGATTCCACGTCA
CTATTTCTCTTTGGGAGAGATACGAAATGTGGAAACAAATCAGTGTCTAGATAACATGGCTAGAAAAGAGAATGAAAAAG
TTGGAATTTTTAACTGTCATGGTATGGGAGGTAATCAGGTTTTCTCTTACACTGCCAACAAAGAAATTAGTACAGATGAC
CTTTGCTTGGATGTCTCCAAACTTAATGGCCCAGTCACAATGCTCAAATGCCACCACCTAAAAGGCAACCAGCTTTGGGA
CTATGACCCGGTGAAATTGACCCTGCAGCATGTGAACAGTAACCAGTGCCTGGACAAAGCCACAGACGAGGACAGCCAGG
TGCCCAGCATCAGAGACTGCAGCGGAAGCCGATCCCAGCAGTGGCTTCTTCGGAACGTCACCCTTCCAGAAATATTC

Alignment

ORF - retro_btau_581 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.67 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MRKFAYCKVVLATSLIWVLLDMFLLLYFSECNKCDEKKERGLPAGDVLEPVQKPHEGPGEMGKPVVIPKE
          MRKFAYCKVVLATSLIWVLLDMFLLLYFSECNKCD...ERGLPAGDVLEPVQKPHEGPGEMGKPVVIPK.
Retrocopy MRKFAYCKVVLATSLIWVLLDMFLLLYFSECNKCDXXXERGLPAGDVLEPVQKPHEGPGEMGKPVVIPKQ

Parental  DQEKMKEMFKINQFNLMASEMIALNRSLPDVRLEGCKTKVYPDNLPTTSVVIVFHNEAWSTLLRTVHSVI
          DQEKMK.MFKINQFNLMASEMIALNRSLPDVRLEGCKTKVYP.NLPTTSVVIVFHNEAWSTLLRTVHS.I
Retrocopy DQEKMKDMFKINQFNLMASEMIALNRSLPDVRLEGCKTKVYPNNLPTTSVVIVFHNEAWSTLLRTVHSII

Parental  NRSPRHMLEEIVLVDDASERDFLKRPLESYVKKLKVPVHVIRMEQRSGLIRARLKGAAVSKGQVITFLDA
          N.SPRHMLEEIVLVDDASERDFLKRPLES.VKKLKVPVHVIRMEQRSGLIRARLKGAAVSKGQV.TFLDA
Retrocopy NHSPRHMLEEIVLVDDASERDFLKRPLES*VKKLKVPVHVIRMEQRSGLIRARLKGAAVSKGQVTTFLDA

Parental  HCECTVGWLEPLLARIKHDRKTVVCPIIDVISDDTFEYMAGSDMTYGGFNWKLNFRWYPVPQREMDRRKG
          HCECTVGWLEPLLARIKHDRKTVVCPIIDVISDDTFEYMAGSDMTYGGFNWKLNFRWYPVPQREMDRRKG
Retrocopy HCECTVGWLEPLLARIKHDRKTVVCPIIDVISDDTFEYMAGSDMTYGGFNWKLNFRWYPVPQREMDRRKG

Parental  DRTLPVRTPTMAGGLFSIDRDYFQEIGTYDAGMDIWGGENLEISFRIWQCGGTLEIVTCSHVGHVFRKAT
          DRTLPVRTPTMAGGLFSIDRDYFQE.GTYDAGMDIWGGENLEISFRIWQCGGTLEIVTCSHVGHVFRKAT
Retrocopy DRTLPVRTPTMAGGLFSIDRDYFQETGTYDAGMDIWGGENLEISFRIWQCGGTLEIVTCSHVGHVFRKAT

Parental  PYTFPGGTGQIINKNNRRLAEVWMDEFKNFFYIISPGVTKVDYGDISSRLGLRHKLQCRPFSWYLENIYP
          PYTFPGGTGQIINKNNRRLAEVWMDEFKNFFYIISPGVTKVDYGDISSRLGLRHKLQCRPFSWYLENIYP
Retrocopy PYTFPGGTGQIINKNNRRLAEVWMDEFKNFFYIISPGVTKVDYGDISSRLGLRHKLQCRPFSWYLENIYP

Parental  DSQIPRHYFSLGEIRNVETNQCLDNMARKENEKVGIFNCHGMGGNQVFSYTANKEIRTDDLCLDVSKLNG
          DSQIPRHYFSLGEIRNVETNQCLDNMARKENEKVGIFNCHGMGGNQVFSYTANKEI.TDDLCLDVSKLNG
Retrocopy DSQIPRHYFSLGEIRNVETNQCLDNMARKENEKVGIFNCHGMGGNQVFSYTANKEISTDDLCLDVSKLNG

Parental  PVTMLKCHHLKGNQLWEYDPVKLTLQHVNSNQCLDKATDEDSQVPSIRDCSGSRSQQWLLRNVTLPEIF
          PVTMLKCHHLKGNQLW.YDPVKLTLQHVNSNQCLDKATDEDSQVPSIRDCSGSRSQQWLLRNVTLPEIF
Retrocopy PVTMLKCHHLKGNQLWDYDPVKLTLQHVNSNQCLDKATDEDSQVPSIRDCSGSRSQQWLLRNVTLPEIF

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	0.29 RPM	13.27 RPM
ERP005899_muscle	0.58 RPM	48.35 RPM
SRP017611_brain	1.23 RPM	17.45 RPM
SRP017611_kidney	1.01 RPM	23.53 RPM
SRP017611_liver	0.91 RPM	20.84 RPM
SRP030211_testis	0.10 RPM	12.91 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

1 EST(s) were mapped to retro_btau_581 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
DY148615	48308663	48308906	100	243	0	243

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_581 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_581 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000009037	1 retrocopy	retro_btau_1410,
Bos taurus	ENSBTAG00000011206	1 retrocopy	retro_btau_581 ,
Callithrix jacchus	ENSCJAG00000021030	2 retrocopies	retro_cjac_1554, retro_cjac_865,
Myotis lucifugus	ENSMLUG00000001978	1 retrocopy	retro_mluc_163,
Mus musculus	ENSMUSG00000000420	1 retrocopy	retro_mmus_1312,
Ictidomys tridecemlineatus	ENSSTOG00000003311	1 retrocopy	retro_itri_954,
Tarsius syrichta	ENSTSYG00000014610	1 retrocopy	retro_tsyr_1444,