RetrogeneDB ID: retro_btau_840

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 2:122343233..122344580(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000040518
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: TUBA1C
• Ensembl ID: ENSBTAG00000039992
• Aliases: TUBA1C, TUBA1, TUBA4A
• Description: Tubulin alpha-1C chain [Source:UniProtKB/Swiss-Prot;Acc:Q3ZCJ7]

Sequence

>retro_btau_840
ATGCGTGAGTGCATCTCCATCCACGTTGGCCAGGCTGGTGTCCAGATCGGCAATGCCTGCTGGGAGCTCTACTGCCTGGA
ACACGGCATTCAGCCCGATGGCCAGATGCCAAGTGACAAGACTATTGGGGGAGGAGACGACTCCTTCAACACCTTCTTCA
GTGAGACGGGTGCTGGCAAGCATGTGCCCAGGGCAGTGTTTGTAGACCTGGAACCCACAGTCATTGATGAGGTGCGCACT
GGCACCTACCGCCAGCTCTTCCACCCTGAGCAACTTATCTCAGGCAAAGAAGATGCCGCCAATAACTATGCCCGAGGTCA
CTACACCATTGGCAAGGAGATCATTGACCTCGTCTTGGACCGAGTTCGGAAACTGGCTGACCAGTGCACGGGTCTTCAGG
GCTTCTTGGTTTTCCACAGCTTTGGTGGGGGAACTGGTTCTGGGTTCACCTCCCTGCTGATGGAACGCCTCTCTGTCGAT
TATGGCAAGAAGTCCAAGCTGGAGTTCTCCATTTACCCAGCCCCCCAGGTTTCCACAGCTGTCGTTGAGCCCTACAACTC
CATCCTCACCACCCACACCACCCTGGAGCACTCTGATTGTGCCTTCATGGTAGACAATGAGGCCATCTATGACATCTGCC
GTAGAAACCTCAACATTGAGCGCCCAACCTACACAAATCTTAACCGCCTCATGAGCCAGATAGTGTCCTCCATCACTGCT
TCCCTGAGGTTTGATGGCGCCCTGAATGTGGATCTGACAGAGTTCCAGACCAACCTGGTGCCCTATCCCCGCACCCACTT
CCCTCTGGCCACATACGCCCCTGTCATCTCTGCTGAGAAAGCCTACCATGAACAGCTTTCTGTAGCAGAGATCACCAATG
CTTGCTTTGAGCCAGCCAACCAGATGGTGAAATGTGACCCTCGCCATGGGAAATACATGGCCTGCTGCCTGTTGTACCGT
GGTGACGTGGTTCCCAAAGATGTCAATGCTGCCATTGCCACCATCAAGACCGAGCGTACCATCCAGTTTGTGGACTGGTG
CCCCACTGGCTTCAAGGTTGGCATTAACTACCAGCCTCCCACTGTGGTACCTGGCGGAGACCTGGCCAAAGTACAGCGAG
CTGTGTGCATGCTGAGCAACACCACAGCTGTTGCTGAGGCCTGGGCGCGCCTGGACCACAAGTTTGACCTGATGTATGCC
AAGCGTGCCTTTGTTCACTGGTACGTGGGTGAGGGCATGGAGGAAGGAGAGTTTTCTGAGGCCCGTGAGGACATGGCTGC
CCTTGAGAAGGATTATGAGGAGGTTGGAGCCGACAGTGCAGAGGGAGATGATGAGGGTGACGAGTAT

Alignment

ORF - retro_btau_840 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.33 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGKHVPRAVFVDL
          MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGKHVPRAVFVDL
Retrocopy MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGKHVPRAVFVDL

Parental  EPTVIDEVRTGTYRQLFHPEQLISGKEDAANNYARGHYTIGKEIIDLVLDRVRKLADQCTGLQGFLVFHS
          EPTVIDEVRTGTYRQLFHPEQLISGKEDAANNYARGHYTIGKEIIDLVLDRVRKLADQCTGLQGFLVFHS
Retrocopy EPTVIDEVRTGTYRQLFHPEQLISGKEDAANNYARGHYTIGKEIIDLVLDRVRKLADQCTGLQGFLVFHS

Parental  FGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTAVVEPYNSILTTHTTLEHSDCAFMVDNEAIY
          FGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTAVVEPYNSILTTHTTLEHSDCAFMVDNEAIY
Retrocopy FGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTAVVEPYNSILTTHTTLEHSDCAFMVDNEAIY

Parental  DICRRNLDIERPTYTNLNRLMSQIVSSITASLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEK
          DICRRNL.IERPTYTNLNRLMSQIVSSITASLRFDGALNVDLTEFQTNLVPYPR.HFPLATYAPVISAEK
Retrocopy DICRRNLNIERPTYTNLNRLMSQIVSSITASLRFDGALNVDLTEFQTNLVPYPRTHFPLATYAPVISAEK

Parental  AYHEQLSVAEITNACFEPANQMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRTIQFVDWCPTG
          AYHEQLSVAEITNACFEPANQMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKT.RTIQFVDWCPTG
Retrocopy AYHEQLSVAEITNACFEPANQMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTERTIQFVDWCPTG

Parental  FKVGINYQPPTVVPGGDLAKVQRAVCMLSNTTAVAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSE
          FKVGINYQPPTVVPGGDLAKVQRAVCMLSNTTAVAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSE
Retrocopy FKVGINYQPPTVVPGGDLAKVQRAVCMLSNTTAVAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSE

Parental  AREDMAALEKDYEEVGADSAEGDDEGDEY
          AREDMAALEKDYEEVGADSAEGDDEGDEY
Retrocopy AREDMAALEKDYEEVGADSAEGDDEGDEY

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	1.30 RPM	2.23 RPM
ERP005899_muscle	9.19 RPM	23.23 RPM
SRP017611_brain	1.69 RPM	1.23 RPM
SRP017611_kidney	5.93 RPM	13.51 RPM
SRP017611_liver	4.23 RPM	7.48 RPM
SRP030211_testis	0.83 RPM	10.42 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_840 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_840 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_840 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 15 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000001489	3 retrocopies	retro_btau_251, retro_btau_350, retro_btau_929,
Bos taurus	ENSBTAG00000012244	1 retrocopy	retro_btau_402,
Bos taurus	ENSBTAG00000039992	1 retrocopy	retro_btau_840 ,
Canis familiaris	ENSCAFG00000008661	2 retrocopies	retro_cfam_960, retro_cfam_978,
Choloepus hoffmanni	ENSCHOG00000008444	2 retrocopies	retro_chof_179, retro_chof_360,
Equus caballus	ENSECAG00000009504	1 retrocopy	retro_ecab_1041,
Erinaceus europaeus	ENSEEUG00000004068	1 retrocopy	retro_eeur_669,
Felis catus	ENSFCAG00000024852	1 retrocopy	retro_fcat_361,
Felis catus	ENSFCAG00000028689	3 retrocopies	retro_fcat_1802, retro_fcat_254, retro_fcat_798,
Macropus eugenii	ENSMEUG00000010779	2 retrocopies	retro_meug_1648, retro_meug_2174,
Mus musculus	ENSMUSG00000043091	1 retrocopy	retro_mmus_843,
Oryctolagus cuniculus	ENSOCUG00000028032	1 retrocopy	retro_ocun_111,
Otolemur garnettii	ENSOGAG00000009435	1 retrocopy	retro_ogar_240,
Pteropus vampyrus	ENSPVAG00000004646	1 retrocopy	retro_pvam_929,
Rattus norvegicus	ENSRNOG00000015544	3 retrocopies	retro_rnor_1193, retro_rnor_2260, retro_rnor_960,